Take a look and make sure you don't have any kinks or blockages in the tubing from the hull fitting to the pump. The Jabsco "intelligent timer" will shut-off the pump if it senses a blockage in the tube. See the jabsco guide attached. There is a flow chart / troubleshooting guide. If that's not it you might just be running into the general unreliability of the timer modules. There is a fix for that in this thread.

Had a chance to look at pumps. Impellers are still good. Having trouble telling timer setting as it doesn't seem to want to enter program mode in 5 sequences all the time. I think my timers are good. tr6coug can you please PM price for re-program. Not sure I'll do it this year but let's see. The port motor does sound rougher than the stbd. Maybe the windings or bearing are the issue? Can the motors be rebuilt rather than buying a whole new pump? I do need to flip them around as they are mounted motor down.

treiter - Yes, the pumps can be rebuilt in most cases. I should have the parts you need, just click on my website link in my signature. Here is a good thread with pictures on how to take the pumps apart.